Variant report

Variant	rs12619242
Chromosome Location	chr2:173376080-173376081
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10174809	0.87[CHB][hapmap];0.81[ASN][1000 genomes]
rs10175670	0.85[JPT][hapmap]
rs10195932	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs10197251	0.82[JPT][hapmap]
rs10497381	0.82[JPT][hapmap]
rs10497385	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1076595	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12465295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12465442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12467358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12469875	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs12469958	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12474168	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12474995	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12475916	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12476126	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12477247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12477594	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12478465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12622687	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13383151	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13402061	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1344272	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1574247	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860377	0.82[JPT][hapmap]
rs16860543	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16860805	1.00[CEU][hapmap]
rs16860809	1.00[CEU][hapmap]
rs2084732	1.00[CEU][hapmap]
rs2178474	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293646	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293649	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2357415	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34094408	0.94[ASN][1000 genomes]
rs3749148	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs3762619	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs3792257	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3792260	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3934627	0.85[JPT][hapmap]
rs4281870	0.83[EUR][1000 genomes]
rs4308101	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4480959	0.82[JPT][hapmap]
rs4619573	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs4972515	1.00[CEU][hapmap]
rs4972839	0.86[ASN][1000 genomes]
rs4972851	1.00[CEU][hapmap]
rs56084828	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57418091	0.87[EUR][1000 genomes]
rs57957394	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58016698	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58044442	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59020762	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59524026	0.85[ASN][1000 genomes]
rs59610589	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60275829	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60442917	0.85[ASN][1000 genomes]
rs60446415	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61542159	0.89[EUR][1000 genomes]
rs6718477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6755100	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72894386	0.86[ASN][1000 genomes]
rs733331	1.00[CEU][hapmap]
rs7564591	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7564654	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7565216	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582972	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7591883	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7609465	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173347800-173376200	Weak transcription	Fetal Heart	heart
2	chr2:173356400-173379200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:173356800-173376200	Weak transcription	Brain Substantia Nigra	brain
4	chr2:173357200-173376600	Weak transcription	Right Ventricle	heart
5	chr2:173357600-173376200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:173358000-173376200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:173369800-173376600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr2:173372400-173377000	Weak transcription	Thymus	Thymus
9	chr2:173372600-173379600	Enhancers	Primary B cells from peripheral blood	blood
10	chr2:173373200-173376200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:173373200-173376200	Weak transcription	NHEK	skin
12	chr2:173373200-173376400	Weak transcription	Fetal Thymus	thymus
13	chr2:173373400-173376400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:173373600-173376400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr2:173374200-173376400	Enhancers	Primary T cells fromperipheralblood	blood
16	chr2:173374200-173376600	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr2:173374800-173376600	Strong transcription	HSMMtube	muscle
18	chr2:173375000-173376400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:173375000-173380800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:173375200-173376400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr2:173375200-173377600	ZNF genes & repeats	GM12878-XiMat	blood
22	chr2:173375400-173376600	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr2:173375400-173376800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:173375400-173378400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
25	chr2:173375400-173378800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
26	chr2:173375400-173379200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:173375600-173376200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:173375600-173376400	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr2:173375600-173376600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr2:173375600-173376600	ZNF genes & repeats	HSMM	muscle
31	chr2:173375600-173378400	ZNF genes & repeats	Liver	Liver
32	chr2:173375800-173376200	Enhancers	Primary B cells from cord blood	blood
33	chr2:173375800-173376600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
34	chr2:173375800-173376600	Enhancers	Primary T cells from cord blood	blood
35	chr2:173375800-173376600	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr2:173375800-173377600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
37	chr2:173376000-173376200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
38	chr2:173376000-173376600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:173376000-173376600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
40	chr2:173376000-173377000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
41	chr2:173376000-173377200	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
42	chr2:173376000-173378400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
43	chr2:173376000-173378800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
44	chr2:173376000-173379000	ZNF genes & repeats	Primary hematopoietic stem cells	blood

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